The example simulation provided with DFBSIM can be run as follows. Navigate to examples/iJR904. Type
make
in the command line to create the executable iJR904. Typing
examples/iJR904
runs the simulation. Alternatively, the simulation can be generated and executed by running the shell script runDFBSIM, through typing
./runDFBSIM.sh
which first compiles the model files together with additional files generated DAEPACK, then executes the compiled simulation file iJR904 and, after successful simulation, generates the plots of cell concentrations, external metabolites and a subset of the flux distribution. The gnuplot package is required to generate the plots.
The results of the simulation are saved in the following text files:

• dsl48lpr.states: The time (t) and evolution of the dynamics states (x), e.g. volume, biomass and external metabolite concentrations.
• primals.data: Time evolution of an element of the flux distribution that was used during integration, i.e. an optimal solution of the embedded LP
• events.data: Accurate time of basis change events and other user defined events (state and time events).

A simple Matlab script that implements the direct approach for this example can be found here.